Nonthermal hard X-ray excess in the Coma cluster: resolving the discrepancy between the results of different PDS data analyses

The detection of a nonthermal excess in the Coma cluster spectrum by two BeppoSAX observations analyzed with the XAS package (Fusco-Femiano et al.) has been disavowed by an analysis (Rossetti & Molendi) performed with a different software package (SAXDAS) for the extraction of the spectrum. To resolve this discrepancy we reanalyze the PDS data considering the same software used by Rossetti & Molendi. A correct selection of the data and the exclusion of contaminating sources in the background determination show that also the SAXDAS analysis reports a nonthermal excess with respect to the thermal emission at about the same confidence level of that obtained with the XAS package (~4.8sigma). Besides, we report the lack of the systematic errors investigated by Rossetti & Molendi and Nevalainen et al. taking into account the whole sample of the PDS observations off the Galactic plane, as already shown in our data analysis of Abell 2256 (Fusco-Femiano, Landi & Orlandini). All this eliminates any ambiguity and confirms the presence of a hard tail in the spectrum of the Coma cluster.Comment: 12 pages, 2 figures. Accepted for publication in ApJ Letter

Polymer Dissolution Model: An Energy Adaptation Of The Critical Ionization Theory

The current scale of features size in the microelectronics industry has reached the point where molecular level interactions affect process fidelity and produce excursions from the continuum world like line edge roughness (LER). Here we present a 3D molecular level model based on the adaptation of the critical ionization (CI) theory using a fundamental interaction energy approach. The model asserts that it is the favorable interaction between the ionized part of the polymer and the developer solution which renders the polymer soluble. Dynamic Monte Carlo methods were used in the current model to study the polymer dissolution phenomenon. The surface ionization was captured by employing an electric double layer at the interface, and polymer motion was simulated using the Metropolis algorithm. The approximated interaction parameters, for different species in the system, were obtained experimentally and used to calibrate the simulated dissolution rate response to polymer molecular weight and developer concentration. The predicted response is in good agreement with experimental dissolution rate data. The simulation results support the premise of the CI theory and provide an insight into the CI model from a new prospective. This model may provide a means to study the contribution of development to LER and other related defects based on molecular level interactions between distinct components in the polymer and the developer.Chemical Engineerin

Modeling Solar Lyman Alpha Irradiance

Solar Lyman alpha irradiance is estimated from various solar indices using linear regression analyses. Models developed with multiple linear regression analysis, including daily values and 81-day running means of solar indices, predict reasonably well both the short- and long-term variations observed in Lyman alpha. It is shown that the full disk equivalent width of the He line at 1083 nm offers the best proxy for Lyman alpha, and that the total irradiance corrected for sunspot effect also has a high correlation with Lyman alpha

A Note on Encodings of Phylogenetic Networks of Bounded Level

Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees, clusters, and triplets, respectively. Thus it is not surprising that many network approaches aim to reconstruct a phylogenetic network from such collections. Related to the well-studied perfect phylogeny problem, the following question is of fundamental importance in this context: When does one of the above collections encode (i.e. uniquely describe) the network that induces it? In this note, we present a complete answer to this question for the special case of a level-1 (phylogenetic) network by characterizing those level-1 networks for which an encoding in terms of one (or equivalently all) of the above collections exists. Given that this type of network forms the first layer of the rich hierarchy of level-k networks, k a non-negative integer, it is natural to wonder whether our arguments could be extended to members of that hierarchy for higher values for k. By giving examples, we show that this is not the case

Solar Irradiance Variations on Active Region Time Scales

The variations of the total solar irradiance is an important tool for studying the Sun, thanks to the development of very precise sensors such as the ACRIM instrument on board the Solar Maximum Mission. The largest variations of the total irradiance occur on time scales of a few days are caused by solar active regions, especially sunspots. Efforts were made to describe the active region effects on total and spectral irradiance

DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli

<p>Abstract</p> <p>Background</p> <p>Manufacturing large quantities of recombinant RNAs by overexpression in a bacterial host is hampered by their instability in intracellular environment. To overcome this problem, an RNA of interest can be fused into a stable bacterial RNA for the resulting chimeric construct to accumulate in the cytoplasm to a sufficiently high level. Being supplemented with cost-effective procedures for isolation of the chimera from cells and recovery of the recombinant RNA from stabilizing scaffold, this strategy might become a viable alternative to the existing methods of chemical or enzymatic RNA synthesis.</p> <p>Results</p> <p>Sequence encoding a 71-nucleotide recombinant RNA was inserted into a plasmid-borne deletion mutant of the <it>Vibrio proteolyticus </it>5S rRNA gene in place of helix III - loop C segment of the original 5S rRNA. After transformation into <it>Escherichia coli</it>, the chimeric RNA (3×<it>pen </it>aRNA) was expressed constitutively from <it>E. coli rrnB </it>P1 and P2 promoters. The RNA chimera accumulated to levels that exceeded those of the host's 5S rRNA. A novel method relying on liquid-solid partitioning of cellular constituents was developed for isolation of total RNA from bacterial cells. This protocol avoids toxic chemicals, and is therefore more suitable for large scale RNA purification than traditional methods. A pair of biotinylated 8-17 DNAzymes was used to bring about the quantitative excision of the 71-nt recombinant RNA from the chimera. The recombinant RNA was isolated by sequence-specific capture on beads with immobilized complementary deoxyoligonucleotide, while DNAzymes were recovered by biotin affinity chromatography for reuse.</p> <p>Conclusions</p> <p>The feasibility of a fermentation-based approach for manufacturing large quantities of small RNAs <it>in vivo </it>using a "5S rRNA scaffold" strategy is demonstrated. The approach provides a route towards an economical method for the large-scale production of small RNAs including shRNAs, siRNAs and aptamers for use in clinical and biomedical research.</p

DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli

Background: Manufacturing large quantities of recombinant RNAs by overexpression in a bacterial host is hampered by their instability in intracellular environment. To overcome this problem, an RNA of interest can be fused into a stable bacterial RNA for the resulting chimeric construct to accumulate in the cytoplasm to a sufficiently high level. Being supplemented with cost-effective procedures for isolation of the chimera from cells and recovery of the recombinant RNA from stabilizing scaffold, this strategy might become a viable alternative to the existing methods of chemical or enzymatic RNA synthesis. Results: Sequence encoding a 71-nucleotide recombinant RNA was inserted into a plasmid-borne deletion mutant of the Vibrio proteolyticus 5S rRNA gene in place of helix III - loop C segment of the original 5S rRNA. After transformation into Escherichia coli, the chimeric RNA (3譸en aRNA) was expressed constitutively from E. coli rrnB P1 and P2 promoters. The RNA chimera accumulated to levels that exceeded those of the host's 5S rRNA. A novel method relying on liquid solid partitioning of cellular constituents was developed for isolation of total RNA from bacterial cells. This protocol avoids toxic chemicals, and is therefore more suitable for large scale RNA purification than traditional methods. A pair of biotinylated 8-17 DNAzymes was used to bring about the quantitative excision of the 71-nt recombinant RNA from the chimera. The recombinant RNA was isolated by sequence-specific capture on beads with immobilized complementary deoxyoligonucleotide, while DNAzymes were recovered by biotin affinity chromatography for reuse. Conclusions:The feasibility of a fermentation-based approach for manufacturing large quantities of small RNAs in vivo using a "5S rRNA scaffold" strategy is demonstrated. The approach provides a route towards an economical method for the large-scale production of small RNAs including shRNAs, siRNAs and aptamers for use in clinical and biomedical research

Folding and unfolding phylogenetic trees and networks

Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network $N$ can be "unfolded" to obtain a MUL-tree $U(N)$ and, conversely, a MUL-tree $T$ can in certain circumstances be "folded" to obtain a phylogenetic network $F(T)$ that exhibits $T$. In this paper, we study properties of the operations $U$ and $F$ in more detail. In particular, we introduce the class of stable networks, phylogenetic networks $N$ for which $F(U(N))$ is isomorphic to $N$, characterise such networks, and show that they are related to the well-known class of tree-sibling networks.We also explore how the concept of displaying a tree in a network $N$ can be related to displaying the tree in the MUL-tree $U(N)$. To do this, we develop a phylogenetic analogue of graph fibrations. This allows us to view $U(N)$ as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in $U(N)$ and reconcilingphylogenetic trees with networks

Polymer Bound Photobase Generators And Photoacid Generators For Pitch Division Lithography

The semiconductor industry is pursuing several process options that provide pathways to printing images smaller than the theoretical resolution limit of 193 nm projection scanners. These processes include double patterning, side wall deposition and pitch division. Pitch doubling lithography (PDL), the achievement of pitch division by addition of a photobase generator (PBG) to typical 193 nm resist formulations was recently presented. 1 Controlling the net acid concentration as a function of dose by incorporating both a photoacid generator (PAG) and a PBG in the resist formulation imparts a resist dissolution rate response modulation at twice the frequency of the aerial image. Simulation and patterning of 45 nm half pitch L/S patterns produced using a 90 nm half pitch mask were reported. 2 Pitch division was achieved, but the line edge roughness of the resulting images did not meet the current standard. To reduce line edge roughness, polymer bound PBGs and polymer bound PAGs were investigated in the PDL resist formulations. The synthesis, purification, analysis, and functional performance of various polymers containing PBG or PAG monomers are described herein. Both polymer bound PBG with monomeric PAG and polymer bound PAG with monomeric PBG showed a PDL response. The performance of the polymer bound formulations is compared to the same formulations with small molecule analogs of PAG and PBG.Chemical Engineerin